[INFO   ] Starting gmx_MMPBSA v1.6.3
[DEBUG  ] WDIR          : /media/romi/Zeus - 1 TB/May 28th - 4 PDBs/7dv4 (July 2023)/7dv4-500ns-extend-312k/free energy
[DEBUG  ] AMBERHOME     : /home/romi/miniconda3/envs/gmxMMPBSA
[DEBUG  ] PYTHON EXE    : /home/romi/miniconda3/envs/gmxMMPBSA/bin/python
[DEBUG  ] PYTHON VERSION: 3.10.14 | packaged by conda-forge | (main, Mar 20 2024, 12:45:18) [GCC 12.3.0]
[DEBUG  ] MPI           : /home/romi/miniconda3/envs/gmxMMPBSA/bin/mpirun
[DEBUG  ] ParmEd        : 4.2.2
[DEBUG  ] OS PLATFORM   : Linux-5.15.0-107-generic-x86_64-with-glibc2.31
[DEBUG  ] OS SYSTEM     : Linux
[DEBUG  ] OS VERSION    : #117~20.04.1-Ubuntu SMP Tue Apr 30 10:35:57 UTC 2024
[DEBUG  ] OS PROCESSOR  : x86_64

[INFO   ] Command-line
  gmx_MMPBSA -O -i mmpbsa.in -cs md_0_10.tpr -ci index.ndx -cg 15 16 -ct dynamic-nopbc.xtc -cp topol.top

[DEBUG  ] |Input file:
[DEBUG  ] |--------------------------------------------------------------
[DEBUG  ] |Input file generated by gmx_MMPBSA (v1.5.2)
[DEBUG  ] |Be careful with the variables you modify, some can have severe consequences on the results you obtain.
[DEBUG  ] |
[DEBUG  ] |# General namelist variables
[DEBUG  ] |&general
[DEBUG  ] |  sys_name             = ""                                             # System name
[DEBUG  ] |  startframe           = 10                                             # First frame to analyze
[DEBUG  ] |  endframe             = 49000                                       # Last frame to analyze
[DEBUG  ] |  interval             = 1000                                        # Number of frames between adjacent frames analyzed
[DEBUG  ] |  forcefields          = "oldff/leaprc.ff99SB,leaprc.gaff"              # Define the force field to build the Amber topology
[DEBUG  ] |  ions_parameters      = 1                                              # Define ions parameters to build the Amber topology
[DEBUG  ] |  PBRadii              = 3                                              # Define PBRadii to build amber topology from GROMACS files
[DEBUG  ] |  temperature          = 312                                        # Temperature
[DEBUG  ] |  qh_entropy           = 0                                              # Do quasi-harmonic calculation
[DEBUG  ] |  interaction_entropy  = 0                                              # Do Interaction Entropy calculation
[DEBUG  ] |  ie_segment           = 25                                             # Trajectory segment to calculate interaction entropy
[DEBUG  ] |  c2_entropy           = 0                                              # Do C2 Entropy calculation
[DEBUG  ] |  assign_chainID       = 0                                              # Assign chains ID
[DEBUG  ] |  exp_ki               = 0.0                                            # Experimental Ki in nM
[DEBUG  ] |  full_traj            = 0                                              # Print a full traj. AND the thread trajectories
[DEBUG  ] |  gmx_path             = ""                                             # Force to use this path to get GROMACS executable
[DEBUG  ] |  keep_files           = 2                                              # How many files to keep after successful completion
[DEBUG  ] |  netcdf               = 0                                              # Use NetCDF intermediate trajectories
[DEBUG  ] |  solvated_trajectory  = 1                                              # Define if it is necessary to cleanup the trajectories
[DEBUG  ] |  verbose              = 1                                              # How many energy terms to print in the final output
[DEBUG  ] |/
[DEBUG  ] |
[DEBUG  ] |# (AMBER) Generalized-Born namelist variables
[DEBUG  ] |&gb
[DEBUG  ] |  igb                  = 5                                              # GB model to use
[DEBUG  ] |  intdiel              = 1.0                                            # Internal dielectric constant for sander
[DEBUG  ] |  extdiel              = 78.5                                           # External dielectric constant for sander
[DEBUG  ] |  saltcon              = 0.0                                            # Salt concentration (M)
[DEBUG  ] |  surften              = 0.0072                                         # Surface tension
[DEBUG  ] |  surfoff              = 0.0                                            # Surface tension offset
[DEBUG  ] |  molsurf              = 0                                              # Use Connelly surface ('molsurf' program)
[DEBUG  ] |  msoffset             = 0.0                                            # Offset for molsurf calculation
[DEBUG  ] |  probe                = 1.4                                            # Solvent probe radius for surface area calc
[DEBUG  ] |  ifqnt                = 0                                              # Use QM on part of the system
[DEBUG  ] |  qm_theory            = ""                                             # Semi-empirical QM theory to use
[DEBUG  ] |  qm_residues          = ""                                             # Residues to treat with QM
[DEBUG  ] |  qmcharge_com         = 0                                              # Charge of QM region in complex
[DEBUG  ] |  qmcharge_lig         = 0                                              # Charge of QM region in ligand
[DEBUG  ] |  qmcharge_rec         = 0                                              # Charge of QM region in receptor
[DEBUG  ] |  qmcut                = 9999.0                                         # Cutoff in the QM region
[DEBUG  ] |  scfconv              = 1e-08                                          # Convergence criteria for the SCF calculation, in kcal/mol
[DEBUG  ] |  peptide_corr         = 0                                              # Apply MM correction to peptide linkages
[DEBUG  ] |  writepdb             = 1                                              # Write a PDB file of the selected QM region
[DEBUG  ] |  verbosity            = 0                                              # Controls the verbosity of QM/MM related output
[DEBUG  ] |  alpb                 = 0                                              # Use Analytical Linearized Poisson-Boltzmann (ALPB)
[DEBUG  ] |  arad_method          = 1                                              # Selected method to estimate the effective electrostatic size
[DEBUG  ] |/
[DEBUG  ] |
[DEBUG  ] |# (AMBER) Possion-Boltzmann namelist variables
[DEBUG  ] |&pb
[DEBUG  ] |  ipb                  = 2                                              # Dielectric model for PB
[DEBUG  ] |  inp                  = 2                                              # Nonpolar solvation method
[DEBUG  ] |  sander_apbs          = 0                                              # Use sander.APBS?
[DEBUG  ] |  indi                 = 1.0                                            # Internal dielectric constant
[DEBUG  ] |  exdi                 = 80.0                                           # External dielectric constant
[DEBUG  ] |  emem                 = 4.0                                            # Membrane dielectric constant
[DEBUG  ] |  smoothopt            = 1                                              # Set up dielectric values for finite-difference grid edges that are located across the solute/solvent dielectric boundary
[DEBUG  ] |  istrng               = 0.0                                            # Ionic strength (M)
[DEBUG  ] |  radiopt              = 1                                              # Use optimized radii?
[DEBUG  ] |  prbrad               = 1.4                                            # Probe radius
[DEBUG  ] |  iprob                = 2.0                                            # Mobile ion probe radius (Angstroms) for ion accessible surface used to define the Stern layer
[DEBUG  ] |  sasopt               = 0                                              # Molecular surface in PB implict model
[DEBUG  ] |  arcres               = 0.25                                           # The resolution (Å) to compute solvent accessible arcs
[DEBUG  ] |  memopt               = 0                                              # Use PB optimization for membrane
[DEBUG  ] |  mprob                = 2.7                                            # Membrane probe radius in Å
[DEBUG  ] |  mthick               = 40.0                                           # Membrane thickness
[DEBUG  ] |  mctrdz               = 0.0                                            # Distance to offset membrane in Z direction
[DEBUG  ] |  poretype             = 1                                              # Use exclusion region for channel proteins
[DEBUG  ] |  npbopt               = 0                                              # Use NonLinear PB solver?
[DEBUG  ] |  solvopt              = 1                                              # Select iterative solver
[DEBUG  ] |  accept               = 0.001                                          # Sets the iteration convergence criterion (relative to the initial residue)
[DEBUG  ] |  linit                = 1000                                           # Number of SCF iterations
[DEBUG  ] |  fillratio            = 4.0                                            # Ratio between the longest dimension of the rectangular finite-difference grid and that of the solute
[DEBUG  ] |  scale                = 2.0                                            # 1/scale = grid spacing for the finite difference solver (default = 1/2 Å)
[DEBUG  ] |  nbuffer              = 0.0                                            # Sets how far away (in grid units) the boundary of the finite difference grid is away from the solute surface
[DEBUG  ] |  nfocus               = 2                                              # Electrostatic focusing calculation
[DEBUG  ] |  fscale               = 8                                              # Set the ratio between the coarse and fine grid spacings in an electrostatic focussing calculation
[DEBUG  ] |  npbgrid              = 1                                              # Sets how often the finite-difference grid is regenerated
[DEBUG  ] |  bcopt                = 5                                              # Boundary condition option
[DEBUG  ] |  eneopt               = 2                                              # Compute electrostatic energy and forces
[DEBUG  ] |  frcopt               = 0                                              # Output for computing electrostatic forces
[DEBUG  ] |  scalec               = 0                                              # Option to compute reaction field energy and forces
[DEBUG  ] |  cutfd                = 5.0                                            # Cutoff for finite-difference interactions
[DEBUG  ] |  cutnb                = 0.0                                            # Cutoff for nonbonded interations
[DEBUG  ] |  nsnba                = 1                                              # Sets how often atom-based pairlist is generated
[DEBUG  ] |  decompopt            = 2                                              # Option to select different decomposition schemes when INP = 2
[DEBUG  ] |  use_rmin             = 1                                              # The option to set up van der Waals radii
[DEBUG  ] |  sprob                = 0.557                                          # Solvent probe radius for SASA used to compute the dispersion term
[DEBUG  ] |  vprob                = 1.3                                            # Solvent probe radius for molecular volume (the volume enclosed by SASA)
[DEBUG  ] |  rhow_effect          = 1.129                                          # Effective water density used in the non-polar dispersion term calculation
[DEBUG  ] |  use_sav              = 1                                              # Use molecular volume (the volume enclosed by SASA) for cavity term calculation
[DEBUG  ] |  cavity_surften       = 0.0378                                         # Surface tension
[DEBUG  ] |  cavity_offset        = -0.5692                                        # Offset for nonpolar solvation calc
[DEBUG  ] |  maxsph               = 400                                            # Approximate number of dots to represent the maximum atomic solvent accessible surface
[DEBUG  ] |  maxarcdot            = 1500                                           # Number of dots used to store arc dots per atom
[DEBUG  ] |  npbverb              = 0                                              # Option to turn on verbose mode
[DEBUG  ] |/
[DEBUG  ] |
[DEBUG  ] |# Decomposition namelist variables
[DEBUG  ] |&decomposition
[DEBUG  ] |  idecomp              = 1                                              # Which type of decomposition analysis to do
[DEBUG  ] |  dec_verbose          = 0                                              # Control energy terms are printed to the output
[DEBUG  ] |  print_res            = "within 6"                                     # Which residues to print decomposition data for
[DEBUG  ] |  csv_format           = 1                                              # Write decomposition data in CSV format
[DEBUG  ] |/
[DEBUG  ] |
[DEBUG  ] |--------------------------------------------------------------
[DEBUG  ] 
[INFO   ] Checking mmpbsa.in input file...
[INFO   ] Checking mmpbsa.in input file...Done.

[INFO   ] Checking external programs...
[INFO   ] cpptraj found! Using /home/romi/miniconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO   ] tleap found! Using /home/romi/miniconda3/envs/gmxMMPBSA/bin/tleap
[INFO   ] parmchk2 found! Using /home/romi/miniconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO   ] sander found! Using /home/romi/miniconda3/envs/gmxMMPBSA/bin/sander
[INFO   ] Using GROMACS version > 5.x.x!
[INFO   ] gmx found! Using /home/romi/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO   ] Checking external programs...Done.

[INFO   ] Building AMBER topologies from GROMACS files...
[INFO   ] Get PDB files from GROMACS structures files...
[INFO   ] Making gmx_MMPBSA index for complex...
[DEBUG  ] Running command: echo -e "name 15 GMXMMPBSA_REC\n name 16 GMXMMPBSA_LIG\n  15 | 16\n q\n" | /home/romi/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx make_ndx -n index.ndx -o _GMXMMPBSA_COM_index.ndx -f md_0_10.tpr
[DEBUG  ]                :-) GROMACS - gmx make_ndx, 2023.4-conda_forge (-:
[DEBUG  ] 
[DEBUG  ] Executable:   /home/romi/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[DEBUG  ] Data prefix:  /home/romi/miniconda3/envs/gmxMMPBSA
[DEBUG  ] Working dir:  /media/romi/Zeus - 1 TB/May 28th - 4 PDBs/7dv4 (July 2023)/7dv4-500ns-extend-312k/free energy
[DEBUG  ] Command line:
[DEBUG  ]   gmx make_ndx -n index.ndx -o _GMXMMPBSA_COM_index.ndx -f md_0_10.tpr
[DEBUG  ] 
[DEBUG  ] 
[DEBUG  ] Reading structure file
[DEBUG  ] Reading file md_0_10.tpr, VERSION 2019.6 (single precision)
[DEBUG  ] Reading file md_0_10.tpr, VERSION 2019.6 (single precision)
[DEBUG  ] 
[DEBUG  ] GROMACS reminds you: "There's only music to make new ringtones" (Arctic Monkeys)
[DEBUG  ] 
[DEBUG  ] Going to read 1 old index file(s)
[DEBUG  ] 
[DEBUG  ]   0 System              : 57262 atoms
[DEBUG  ]   1 Protein             :  3550 atoms
[DEBUG  ]   2 Protein-H           :  1788 atoms
[DEBUG  ]   3 C-alpha             :   238 atoms
[DEBUG  ]   4 Backbone            :   714 atoms
[DEBUG  ]   5 MainChain           :   950 atoms
[DEBUG  ]   6 MainChain+Cb        :  1164 atoms
[DEBUG  ]   7 MainChain+H         :  1183 atoms
[DEBUG  ]   8 SideChain           :  2367 atoms
[DEBUG  ]   9 SideChain-H         :   838 atoms
[DEBUG  ]  10 Prot-Masses         :  3550 atoms
[DEBUG  ]  11 non-Protein         : 53712 atoms
[DEBUG  ]  12 Water               : 53712 atoms
[DEBUG  ]  13 SOL                 : 53712 atoms
[DEBUG  ]  14 non-Water           :  3550 atoms
[DEBUG  ]  15 Chain_A             :  1761 atoms
[DEBUG  ]  16 Chain_B             :  1789 atoms
[DEBUG  ] 
[DEBUG  ]  nr : group      '!': not  'name' nr name   'splitch' nr    Enter: list groups
[DEBUG  ]  'a': atom       '&': and  'del' nr         'splitres' nr   'l': list residues
[DEBUG  ]  't': atom type  '|': or   'keep' nr        'splitat' nr    'h': help
[DEBUG  ]  'r': residue              'res' nr         'chain' char
[DEBUG  ]  "name": group             'case': case sensitive           'q': save and quit
[DEBUG  ]  'ri': residue index
[DEBUG  ] 
[DEBUG  ] > 
[DEBUG  ] 
[DEBUG  ] > 
[DEBUG  ] 
[DEBUG  ] > 
[DEBUG  ] Copied index group 15 'GMXMMPBSA_REC'
[DEBUG  ] Copied index group 16 'GMXMMPBSA_LIG'
[DEBUG  ] Merged two groups with OR: 1761 1789 -> 3550
[DEBUG  ] 
[DEBUG  ] > 
[INFO   ] Normal Complex: Saving group Chain_A_Chain_B (15_16) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[DEBUG  ] Running command: echo -e "GMXMMPBSA_REC_GMXMMPBSA_LIG"| /home/romi/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv -f dynamic-nopbc.xtc -s md_0_10.tpr -o _GMXMMPBSA_COM.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0
[DEBUG  ]                :-) GROMACS - gmx trjconv, 2023.4-conda_forge (-:
[DEBUG  ] 
[DEBUG  ] Executable:   /home/romi/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[DEBUG  ] Data prefix:  /home/romi/miniconda3/envs/gmxMMPBSA
[DEBUG  ] Working dir:  /media/romi/Zeus - 1 TB/May 28th - 4 PDBs/7dv4 (July 2023)/7dv4-500ns-extend-312k/free energy
[DEBUG  ] Command line:
[DEBUG  ]   gmx trjconv -f dynamic-nopbc.xtc -s md_0_10.tpr -o _GMXMMPBSA_COM.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0
[DEBUG  ] 
[DEBUG  ] Will write pdb: Protein data bank file
[DEBUG  ] Reading file md_0_10.tpr, VERSION 2019.6 (single precision)
[DEBUG  ] Reading file md_0_10.tpr, VERSION 2019.6 (single precision)
[DEBUG  ] Group     0 (         System) has 57262 elements
[DEBUG  ] Group     1 (        Protein) has  3550 elements
[DEBUG  ] Group     2 (      Protein-H) has  1788 elements
[DEBUG  ] Group     3 (        C-alpha) has   238 elements
[DEBUG  ] Group     4 (       Backbone) has   714 elements
[DEBUG  ] Group     5 (      MainChain) has   950 elements
[DEBUG  ] Group     6 (   MainChain+Cb) has  1164 elements
[DEBUG  ] Group     7 (    MainChain+H) has  1183 elements
[DEBUG  ] Group     8 (      SideChain) has  2367 elements
[DEBUG  ] Group     9 (    SideChain-H) has   838 elements
[DEBUG  ] Group    10 (    Prot-Masses) has  3550 elements
[DEBUG  ] Group    11 (    non-Protein) has 53712 elements
[DEBUG  ] Group    12 (          Water) has 53712 elements
[DEBUG  ] Group    13 (            SOL) has 53712 elements
[DEBUG  ] Group    14 (      non-Water) has  3550 elements
[DEBUG  ] Group    15 (  GMXMMPBSA_REC) has  1761 elements
[DEBUG  ] Group    16 (  GMXMMPBSA_LIG) has  1789 elements
[DEBUG  ] Group    17 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has  3550 elements
[DEBUG  ] Select a group: Reading frame       0 time    0.000   
[DEBUG  ] Precision of dynamic-nopbc.xtc is 0.001 (nm)
[DEBUG  ] Reading frame       1 time   10.000   
[DEBUG  ] Dumping frame at t= 0 ps
[DEBUG  ] Last written: frame      0 time    0.000
[DEBUG  ] 
[DEBUG  ] 
[DEBUG  ] GROMACS reminds you: "There's only music to make new ringtones" (Arctic Monkeys)
[DEBUG  ] 
[DEBUG  ] Note that major changes are planned in future for trjconv, to improve usability and utility.
[DEBUG  ] Select group for output
[DEBUG  ] Selected 17: 'GMXMMPBSA_REC_GMXMMPBSA_LIG'
[INFO   ] No receptor structure file was defined. Using ST approach...
[INFO   ] Using receptor structure from complex to generate AMBER topology
[INFO   ] Normal Receptor: Saving group Chain_A (15) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[DEBUG  ] Running command: echo -e "15"| /home/romi/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv -f dynamic-nopbc.xtc -s md_0_10.tpr -o _GMXMMPBSA_REC.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0
[DEBUG  ]                :-) GROMACS - gmx trjconv, 2023.4-conda_forge (-:
[DEBUG  ] 
[DEBUG  ] Executable:   /home/romi/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[DEBUG  ] Data prefix:  /home/romi/miniconda3/envs/gmxMMPBSA
[DEBUG  ] Working dir:  /media/romi/Zeus - 1 TB/May 28th - 4 PDBs/7dv4 (July 2023)/7dv4-500ns-extend-312k/free energy
[DEBUG  ] Command line:
[DEBUG  ]   gmx trjconv -f dynamic-nopbc.xtc -s md_0_10.tpr -o _GMXMMPBSA_REC.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0
[DEBUG  ] 
[DEBUG  ] Will write pdb: Protein data bank file
[DEBUG  ] Reading file md_0_10.tpr, VERSION 2019.6 (single precision)
[DEBUG  ] Reading file md_0_10.tpr, VERSION 2019.6 (single precision)
[DEBUG  ] Group     0 (         System) has 57262 elements
[DEBUG  ] Group     1 (        Protein) has  3550 elements
[DEBUG  ] Group     2 (      Protein-H) has  1788 elements
[DEBUG  ] Group     3 (        C-alpha) has   238 elements
[DEBUG  ] Group     4 (       Backbone) has   714 elements
[DEBUG  ] Group     5 (      MainChain) has   950 elements
[DEBUG  ] Group     6 (   MainChain+Cb) has  1164 elements
[DEBUG  ] Group     7 (    MainChain+H) has  1183 elements
[DEBUG  ] Group     8 (      SideChain) has  2367 elements
[DEBUG  ] Group     9 (    SideChain-H) has   838 elements
[DEBUG  ] Group    10 (    Prot-Masses) has  3550 elements
[DEBUG  ] Group    11 (    non-Protein) has 53712 elements
[DEBUG  ] Group    12 (          Water) has 53712 elements
[DEBUG  ] Group    13 (            SOL) has 53712 elements
[DEBUG  ] Group    14 (      non-Water) has  3550 elements
[DEBUG  ] Group    15 (  GMXMMPBSA_REC) has  1761 elements
[DEBUG  ] Group    16 (  GMXMMPBSA_LIG) has  1789 elements
[DEBUG  ] Group    17 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has  3550 elements
[DEBUG  ] Select a group: Reading frame       0 time    0.000   
[DEBUG  ] Precision of dynamic-nopbc.xtc is 0.001 (nm)
[DEBUG  ] Reading frame       1 time   10.000   
[DEBUG  ] Dumping frame at t= 0 ps
[DEBUG  ] Last written: frame      0 time    0.000
[DEBUG  ] 
[DEBUG  ] 
[DEBUG  ] GROMACS reminds you: "There's only music to make new ringtones" (Arctic Monkeys)
[DEBUG  ] 
[DEBUG  ] Note that major changes are planned in future for trjconv, to improve usability and utility.
[DEBUG  ] Select group for output
[DEBUG  ] Selected 15: 'GMXMMPBSA_REC'
[INFO   ] No ligand structure file was defined. Using ST approach...
[INFO   ] Using ligand structure from complex to generate AMBER topology
[INFO   ] Normal Ligand: Saving group Chain_B (16) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[DEBUG  ] Running command: echo -e "16"| /home/romi/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv -f dynamic-nopbc.xtc -s md_0_10.tpr -o _GMXMMPBSA_LIG.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0
[DEBUG  ]                :-) GROMACS - gmx trjconv, 2023.4-conda_forge (-:
[DEBUG  ] 
[DEBUG  ] Executable:   /home/romi/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[DEBUG  ] Data prefix:  /home/romi/miniconda3/envs/gmxMMPBSA
[DEBUG  ] Working dir:  /media/romi/Zeus - 1 TB/May 28th - 4 PDBs/7dv4 (July 2023)/7dv4-500ns-extend-312k/free energy
[DEBUG  ] Command line:
[DEBUG  ]   gmx trjconv -f dynamic-nopbc.xtc -s md_0_10.tpr -o _GMXMMPBSA_LIG.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0
[DEBUG  ] 
[DEBUG  ] Will write pdb: Protein data bank file
[DEBUG  ] Reading file md_0_10.tpr, VERSION 2019.6 (single precision)
[DEBUG  ] Reading file md_0_10.tpr, VERSION 2019.6 (single precision)
[DEBUG  ] Group     0 (         System) has 57262 elements
[DEBUG  ] Group     1 (        Protein) has  3550 elements
[DEBUG  ] Group     2 (      Protein-H) has  1788 elements
[DEBUG  ] Group     3 (        C-alpha) has   238 elements
[DEBUG  ] Group     4 (       Backbone) has   714 elements
[DEBUG  ] Group     5 (      MainChain) has   950 elements
[DEBUG  ] Group     6 (   MainChain+Cb) has  1164 elements
[DEBUG  ] Group     7 (    MainChain+H) has  1183 elements
[DEBUG  ] Group     8 (      SideChain) has  2367 elements
[DEBUG  ] Group     9 (    SideChain-H) has   838 elements
[DEBUG  ] Group    10 (    Prot-Masses) has  3550 elements
[DEBUG  ] Group    11 (    non-Protein) has 53712 elements
[DEBUG  ] Group    12 (          Water) has 53712 elements
[DEBUG  ] Group    13 (            SOL) has 53712 elements
[DEBUG  ] Group    14 (      non-Water) has  3550 elements
[DEBUG  ] Group    15 (  GMXMMPBSA_REC) has  1761 elements
[DEBUG  ] Group    16 (  GMXMMPBSA_LIG) has  1789 elements
[DEBUG  ] Group    17 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has  3550 elements
[DEBUG  ] Select a group: Reading frame       0 time    0.000   
[DEBUG  ] Precision of dynamic-nopbc.xtc is 0.001 (nm)
[DEBUG  ] Reading frame       1 time   10.000   
[DEBUG  ] Dumping frame at t= 0 ps
[DEBUG  ] Last written: frame      0 time    0.000
[DEBUG  ] 
[DEBUG  ] 
[DEBUG  ] GROMACS reminds you: "There's only music to make new ringtones" (Arctic Monkeys)
[DEBUG  ] 
[DEBUG  ] Note that major changes are planned in future for trjconv, to improve usability and utility.
[DEBUG  ] Select group for output
[DEBUG  ] Selected 16: 'GMXMMPBSA_LIG'
[INFO   ] Checking the structures consistency...
[INFO   ] 
[INFO   ] Using topology conversion. Setting radiopt = 0...
[INFO   ] Building Normal Complex Amber topology...
[INFO   ] Detected CHARMM force field topology format...
[INFO   ] Assigning PBRadii mbondi2 to Complex...
[INFO   ] Writing Normal Complex AMBER topology...
[INFO   ] No Receptor topology file was defined. Using ST approach...
[INFO   ] Building AMBER Receptor topology from Complex...
[INFO   ] Assigning PBRadii mbondi2 to Receptor...
[INFO   ] Writing Normal Receptor AMBER topology...
[INFO   ] No Ligand topology file was defined. Using ST approach...
[INFO   ] Building AMBER Ligand topology from Complex...
[INFO   ] Assigning PBRadii mbondi2 to Ligand...
[INFO   ] Writing Normal Ligand AMBER topology...
[INFO   ] Selecting residues by distance (6 Å) between receptor and ligand for decomposition analysis...
[INFO   ] Selected 63 residues:
R:A:GLU:33  R:A:VAL:34  R:A:ARG:35  R:A:THR:37  R:A:VAL:38  R:A:LEU:39  R:A:THR:47  R:A:GLU:48  R:A:VAL:49  R:A:CYS:50
R:A:ALA:51  R:A:ALA:52  R:A:THR:53  R:A:TYR:54  R:A:MET:55  R:A:ASN:58  R:A:GLU:59  R:A:LEU:60  R:A:THR:61  R:A:PHE:62
R:A:LEU:63  R:A:ASP:64  R:A:ASP:65  R:A:SER:66  R:A:ILE:67  R:A:LYS:95  R:A:GLU:97  R:A:LEU:98  R:A:MET:99  R:A:TYR:100
R:A:PRO:101 R:A:PRO:102 R:A:TYR:104 R:A:LEU:106 L:B:GLY:119 L:B:GLU:120 L:B:VAL:121 L:B:GLY:145 L:B:PHE:146 L:B:THR:147
L:B:LYS:150 L:B:ASN:151 L:B:TYR:152 L:B:VAL:169 L:B:TYR:171 L:B:SER:172 L:B:GLY:173 L:B:GLY:174 L:B:SER:175 L:B:LYS:176
L:B:THR:177 L:B:ARG:216 L:B:ALA:217 L:B:VAL:218 L:B:PRO:219 L:B:HIS:220 L:B:SER:221 L:B:PRO:222 L:B:SER:223 L:B:SER:224
L:B:PHE:225 L:B:ASP:226 L:B:ILE:227

[INFO   ] Cleaning normal complex trajectories...
[DEBUG  ] Running command: echo -e "GMXMMPBSA_REC_GMXMMPBSA_LIG"| /home/romi/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv -f dynamic-nopbc.xtc -s md_0_10.tpr -o COM_traj_0.xtc -n _GMXMMPBSA_COM_index.ndx
[DEBUG  ]                :-) GROMACS - gmx trjconv, 2023.4-conda_forge (-:
[DEBUG  ] 
[DEBUG  ] Executable:   /home/romi/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[DEBUG  ] Data prefix:  /home/romi/miniconda3/envs/gmxMMPBSA
[DEBUG  ] Working dir:  /media/romi/Zeus - 1 TB/May 28th - 4 PDBs/7dv4 (July 2023)/7dv4-500ns-extend-312k/free energy
[DEBUG  ] Command line:
[DEBUG  ]   gmx trjconv -f dynamic-nopbc.xtc -s md_0_10.tpr -o COM_traj_0.xtc -n _GMXMMPBSA_COM_index.ndx
[DEBUG  ] 
[DEBUG  ] Will write xtc: Compressed trajectory (portable xdr format): xtc
[DEBUG  ] Reading file md_0_10.tpr, VERSION 2019.6 (single precision)
[DEBUG  ] Reading file md_0_10.tpr, VERSION 2019.6 (single precision)
[DEBUG  ] Group     0 (         System) has 57262 elements
[DEBUG  ] Group     1 (        Protein) has  3550 elements
[DEBUG  ] Group     2 (      Protein-H) has  1788 elements
[DEBUG  ] Group     3 (        C-alpha) has   238 elements
[DEBUG  ] Group     4 (       Backbone) has   714 elements
[DEBUG  ] Group     5 (      MainChain) has   950 elements
[DEBUG  ] Group     6 (   MainChain+Cb) has  1164 elements
[DEBUG  ] Group     7 (    MainChain+H) has  1183 elements
[DEBUG  ] Group     8 (      SideChain) has  2367 elements
[DEBUG  ] Group     9 (    SideChain-H) has   838 elements
[DEBUG  ] Group    10 (    Prot-Masses) has  3550 elements
[DEBUG  ] Group    11 (    non-Protein) has 53712 elements
[DEBUG  ] Group    12 (          Water) has 53712 elements
[DEBUG  ] Group    13 (            SOL) has 53712 elements
[DEBUG  ] Group    14 (      non-Water) has  3550 elements
[DEBUG  ] Group    15 (  GMXMMPBSA_REC) has  1761 elements
[DEBUG  ] Group    16 (  GMXMMPBSA_LIG) has  1789 elements
[DEBUG  ] Group    17 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has  3550 elements
[DEBUG  ] Select a group: Reading frame       0 time    0.000   
[DEBUG  ] Precision of dynamic-nopbc.xtc is 0.001 (nm)
[DEBUG  ] Using output precision of 0.001 (nm)
[DEBUG  ] Reading frame       1 time   10.000    ->  frame      0 time    0.000      Reading frame       2 time   20.000    ->  frame      1 time   10.000      Reading frame       3 time   30.000    ->  frame      2 time   20.000      Reading frame       4 time   40.000    ->  frame      3 time   30.000      Reading frame       5 time   50.000    ->  frame      4 time   40.000      Reading frame       6 time   60.000    ->  frame      5 time   50.000      Reading frame       7 time   70.000    ->  frame      6 time   60.000      Reading frame       8 time   80.000    ->  frame      7 time   70.000      Reading frame       9 time   90.000    ->  frame      8 time   80.000      Reading frame      10 time  100.000    ->  frame      9 time   90.000      Reading frame      11 time  110.000    ->  frame     10 time  100.000      Reading frame      12 time  120.000    ->  frame     11 time  110.000      Reading frame      13 time  130.000    ->  frame     12 time  120.000      Reading frame      14 time  140.000    ->  frame     13 time  130.000      Reading frame      15 time  150.000    ->  frame     14 time  140.000      Reading frame      16 time  160.000    ->  frame     15 time  150.000      Reading frame      17 time  170.000    ->  frame     16 time  160.000      Reading frame      18 time  180.000    ->  frame     17 time  170.000      Reading frame      19 time  190.000    ->  frame     18 time  180.000      Reading frame      20 time  200.000    ->  frame     19 time  190.000      Reading frame      30 time  300.000    ->  frame     29 time  290.000      Reading frame      40 time  400.000    ->  frame     39 time  390.000      Reading frame      50 time  500.000    ->  frame     49 time  490.000      Reading frame      60 time  600.000    ->  frame     59 time  590.000      Reading frame      70 time  700.000    ->  frame     69 time  690.000      Reading frame      80 time  800.000    ->  frame     79 time  790.000      Reading frame      90 time  900.000    ->  frame     89 time  890.000      Reading frame     100 time 1000.000    ->  frame     99 time  990.000      Reading frame     110 time 1100.000    ->  frame    109 time 1090.000      Reading frame     120 time 1200.000    ->  frame    119 time 1190.000      Reading frame     130 time 1300.000    ->  frame    129 time 1290.000      Reading frame     140 time 1400.000    ->  frame    139 time 1390.000      Reading frame     150 time 1500.000    ->  frame    149 time 1490.000      Reading frame     160 time 1600.000    ->  frame    159 time 1590.000      Reading frame     170 time 1700.000    ->  frame    169 time 1690.000      Reading frame     180 time 1800.000    ->  frame    179 time 1790.000      Reading frame     190 time 1900.000    ->  frame    189 time 1890.000      Reading frame     200 time 2000.000    ->  frame    199 time 1990.000      Reading frame     300 time 3000.000    ->  frame    299 time 2990.000      Reading frame     400 time 4000.000    ->  frame    399 time 3990.000      Reading frame     500 time 5000.000    ->  frame    499 time 4990.000      Reading frame     600 time 6000.000    ->  frame    599 time 5990.000      Reading frame     700 time 7000.000    ->  frame    699 time 6990.000      Reading frame     800 time 8000.000    ->  frame    799 time 7990.000      Reading frame     900 time 9000.000    ->  frame    899 time 8990.000      Reading frame    1000 time 10000.000    ->  frame    999 time 9990.000      Reading frame    1100 time 11000.000    ->  frame   1099 time 10990.000      Reading frame    1200 time 12000.000    ->  frame   1199 time 11990.000      Reading frame    1300 time 13000.000    ->  frame   1299 time 12990.000      Reading frame    1400 time 14000.000    ->  frame   1399 time 13990.000      Reading frame    1500 time 15000.000    ->  frame   1499 time 14990.000      Reading frame    1600 time 16000.000    ->  frame   1599 time 15990.000      Reading frame    1700 time 17000.000    ->  frame   1699 time 16990.000      Reading frame    1800 time 18000.000    ->  frame   1799 time 17990.000      Reading frame    1900 time 19000.000    ->  frame   1899 time 18990.000      Reading frame    2000 time 20000.000    ->  frame   1999 time 19990.000      Reading frame    3000 time 30000.000    ->  frame   2999 time 29990.000      Reading frame    4000 time 40000.000    ->  frame   3999 time 39990.000      Reading frame    5000 time 50000.000    ->  frame   4999 time 49990.000      Reading frame    6000 time 60000.000    ->  frame   5999 time 59990.000      Reading frame    7000 time 70000.000    ->  frame   6999 time 69990.000      Reading frame    8000 time 80000.000    ->  frame   7999 time 79990.000      Reading frame    9000 time 90000.000    ->  frame   8999 time 89990.000      Reading frame   10000 time 100000.000    ->  frame   9999 time 99990.000      Reading frame   11000 time 110000.000    ->  frame  10999 time 109990.000      Reading frame   12000 time 120000.000    ->  frame  11999 time 119990.000      Reading frame   13000 time 130000.000    ->  frame  12999 time 129990.000      Reading frame   14000 time 140000.000    ->  frame  13999 time 139990.000      Reading frame   15000 time 150000.000    ->  frame  14999 time 149990.000      Reading frame   16000 time 160000.000    ->  frame  15999 time 159990.000      Reading frame   17000 time 170000.000    ->  frame  16999 time 169990.000      Reading frame   18000 time 180000.000    ->  frame  17999 time 179990.000      Reading frame   19000 time 190000.000    ->  frame  18999 time 189990.000      Reading frame   20000 time 200000.000    ->  frame  19999 time 199990.000      Reading frame   21000 time 210000.000    ->  frame  20999 time 209990.000      Reading frame   22000 time 220000.000    ->  frame  21999 time 219990.000      Reading frame   23000 time 230000.000    ->  frame  22999 time 229990.000      Reading frame   24000 time 240000.000    ->  frame  23999 time 239990.000      Reading frame   25000 time 250000.000    ->  frame  24999 time 249990.000      Reading frame   26000 time 260000.000    ->  frame  25999 time 259990.000      Reading frame   27000 time 270000.000    ->  frame  26999 time 269990.000      Reading frame   28000 time 280000.000    ->  frame  27999 time 279990.000      Reading frame   29000 time 290000.000    ->  frame  28999 time 289990.000      Reading frame   30000 time 300000.000    ->  frame  29999 time 299990.000      Reading frame   31000 time 310000.000    ->  frame  30999 time 309990.000      Reading frame   32000 time 320000.000    ->  frame  31999 time 319990.000      Reading frame   33000 time 330000.000    ->  frame  32999 time 329990.000      Reading frame   34000 time 340000.000    ->  frame  33999 time 339990.000      Reading frame   35000 time 350000.000    ->  frame  34999 time 349990.000      Reading frame   36000 time 360000.000    ->  frame  35999 time 359990.000      Reading frame   37000 time 370000.000    ->  frame  36999 time 369990.000      Reading frame   38000 time 380000.000    ->  frame  37999 time 379990.000      Reading frame   39000 time 390000.000    ->  frame  38999 time 389990.000      Reading frame   40000 time 400000.000    ->  frame  39999 time 399990.000      Reading frame   41000 time 410000.000    ->  frame  40999 time 409990.000      Reading frame   42000 time 420000.000    ->  frame  41999 time 419990.000      Reading frame   43000 time 430000.000    ->  frame  42999 time 429990.000      Reading frame   44000 time 440000.000    ->  frame  43999 time 439990.000      Reading frame   45000 time 450000.000    ->  frame  44999 time 449990.000      Reading frame   46000 time 460000.000    ->  frame  45999 time 459990.000      Reading frame   47000 time 470000.000    ->  frame  46999 time 469990.000      Reading frame   48000 time 480000.000    ->  frame  47999 time 479990.000      Reading frame   49000 time 490000.000    ->  frame  48999 time 489990.000      Reading frame   50000 time 500000.000    ->  frame  49999 time 499990.000      Last frame      50000 time 500000.000   
[DEBUG  ] Last written: frame  50000 time 500000.000
[DEBUG  ] 
[DEBUG  ] 
[DEBUG  ] GROMACS reminds you: "Unlike teachers or doctors, our efforts improve the lives of people we'll never meet." (Katie Busch-Sorensen)
[DEBUG  ] 
[DEBUG  ] Note that major changes are planned in future for trjconv, to improve usability and utility.
[DEBUG  ] Select group for output
[DEBUG  ] Selected 17: 'GMXMMPBSA_REC_GMXMMPBSA_LIG'
[INFO   ] Building AMBER topologies from GROMACS files... Done.

[INFO   ] Loading and checking parameter files for compatibility...
[INFO   ] Preparing trajectories for simulation...

[INFO   ] 49 frames were processed by cpptraj for use in calculation.
[INFO   ] Starting calculations in 1 CPUs...
[INFO   ] Running calculations on normal system...
[INFO   ] Beginning GB calculations with /home/romi/miniconda3/envs/gmxMMPBSA/bin/sander
[INFO   ]   calculating complex contribution...
[INFO   ]   calculating receptor contribution...
[INFO   ]   calculating ligand contribution...
[INFO   ] Beginning PB calculations with /home/romi/miniconda3/envs/gmxMMPBSA/bin/sander
[INFO   ]   calculating complex contribution...
[INFO   ]   calculating receptor contribution...
[INFO   ]   calculating ligand contribution...
[INFO   ] Parsing results to output files...

[INFO   ] Timing:
[INFO   ] Total GROMACS setup time:                   1.114 min.
[INFO   ] Total AMBER setup time:                     0.015 min.
[INFO   ] Creating trajectories with cpptraj:         0.264 min.
[INFO   ] Total calculation time:                    57.535 min.
[INFO   ] Total GB calculation time:                 14.834 min.
[INFO   ] Total PB calculation time:                 42.108 min.
[INFO   ] Statistics calculation & output writing:    0.004 min.
[INFO   ] Total time taken:                          58.946 min.

[INFO   ] 
   Finalizing gmx_MMPBSA: [ERROR  ] = 0; [WARNING] = 0
   Check the gmx_MMPBSA.log file for more details...

[INFO   ] 
 Thank you for using gmx_MMPBSA. Please consider supporting gmx_MMPBSA by citing our publication:
    Valdés-Tresanco, M.S., Valdés-Tresanco, M.E., Valiente, P.A. and Moreno E. 
    gmx_MMPBSA: A New Tool to Perform End-State Free Energy Calculations with GROMACS. 
    J Chem Theory Comput., 2021, 17 (10):6281-6291. Epub 2021 Sep 29. PMID: 34586825.
    https://pubs.acs.org/doi/10.1021/acs.jctc.1c00645

Also consider citing MMPBSA.py:
    Miller III, B. R., McGee Jr., T. D., Swails, J. M. Homeyer, N. Gohlke, H. and Roitberg, A. E.
    MMPBSA.py: An Efficient Program for End-State Free Energy Calculations.
    J. Chem. Theory Comput., 2012, 8 (9) pp 3314-3321

[INFO   ] Opening gmx_MMPBSA_ana to analyze results...

